She began to study brainwashing in the 1950s at Walter Reed Institute of Research in Washington, D.C., where she interviewed U.S. soldiers who had been taken prisoner during the Korean War. She moved to Berkeley in 1958. Dr. Singer began studying cults in the late 1960s.

She was also very active in the fields of communication and family therapy and for eight years; a member of the Board of Directors of Family Process.

One of her stated fields of expertise that made her famous was cults, mind control ("psychological coercion") and similar areas, in which she published prolifically and received a number of honors (Leo J. Ryan Memorial Award, Research Scientist Award, president of the American Psychosomatic Society).

Singer is popularly known for co-writing the book Cults in Our Midst (ISBN 0787967416). Publisher's Weekly wrote: "Clinical psychologist Singer, emeritus professor at Berkeley, and former cult member Lalich (coauthor of Captive Hearts, Captive Minds) here present an instructive report on the cult phenomenon, which they regard as a growing menace around the world. They define cults as organizations that feature 'coordinated programs of coercive influence and behavioral control,' many religiously or politically oriented and increasingly centered on New Age self-improvement techniques that they claim are now being peddled to businesses."

She dominated anti-cult theory (such as her Theory of Systematic Manipulation of Social and Psychological Influence) and was on the board of the American Family Foundation, the major anti-cult group in the United States. She headed the Task Force on Deceptive and Indirect Methods of Persuasion and Control (DIMPAC) in 1987 for the APA. When her findings were rejected by the Board of Social and Ethical Responsibility for Psychology (BSERP) for "[lacking] the scientific rigor and evenhanded critical approach necessary" she sued the APA and lost in 1993. She testified, with variable success, on mind control in numerous trials in the 1980s and 1990s. She was involved with studying Patty Hearst, and the Branch Davidians.

Dr. Margaret Singer died of natural causes on November 23, 2003 in Berkeley, California. She was 82.